The generated phylogenetic tree is missing MAGs at the leaf nodes.

[ylei14]

Hi,
Hope you're doing well.
Thank you for your previous response. The previous issue has been successfully resolved, and I have obtained my phylogenetic tree. However, my leaf nodes cannot fully display my MAGs (some are missing). When I checked the log file, I found this kind of error: "Not enough markers (93/100) found in "/ifs1/User/leiyu/metagenome/Binning_dir/10GTDBtk/Phylophlan/tmp/map_aa/DG23_bin.18.b6o.bz2". After searching online and modifying my script, the problem still persists. Below is my modified script:
#!/bin/bash

echo "Job Start at date"

source ~/mambaforge/bin/activate /ifs1/User/leiyu/mambaforge/envs/phylophlan

phylophlan
-i /ifs1/User/leiyu/metagenome/Binning_dir/112_AA_seq
-t a
-d phylophlan
--diversity medium
-f /ifs1/User/leiyu/biosoft/phylophlan/supermatrix_aa.cfg
--nproc 20
-o /ifs1/User/leiyu/metagenome/Binning_dir/10_GTDBtk/Phylophlan1/
--min_num_markers 45
--proteome_extension .pep

echo "Job End at date"

I originally thought that "--min_num_markers 45" could solve my problem, but the issue still persists, and the number of missing MAGs remains the same before and after adding "--min_num_markers 45". I used Prodigal to predict the protein sequences of the MAGs and built a phylogenetic tree based on the protein sequences. Could you please help me address the above issues?

Looking forward to your reply.
cheers